Method for analyzing partial gene sequences

Abstract

An computer-based iterative method for analyzing partial gene sequences. Putative gene assemblies are built from partial gene sequences by the method. A series of pre-processing steps prior to assembly allows efficient and accurate assembly of large amounts of partial gene sequences.

We claim: 
     
       1. A computer-based iterative method for building putative gene assemblies from a plurality of partial gene sequences, allowing the incremental addition of new partial gene sequences to be integrated with an existing plurality of putative gene assemblies, comprising the steps of: (a) preprocessing the partial gene sequences and existing putative gene assemblies;   (b) assembling, responsive to grouping relationships, a consensus sequence from the preprocessed partial gene sequences and putative gene assemblies; and   (c) generating a sequence;   whereby the preprocessing step allows for efficient and accurate assembly.   
     
     
       2. The method of claim 1 wherein the preprocessing step comprises the steps of: (a)(1) annotating regions within each of the plurality of partial gene sequences and each of the plurality of existing putative gene assemblies; and   (a)(2) grouping annotated partial gene sequences with other annotated partial gene sequences, wherein some of the other annotated partial gene sequences may be components of existing putative gene assemblies.   
     
     
       3. The method of claim 1 further comprising the step of: (d) characterizing the consensus sequence.   
     
     
       4. The method of claim 3 wherein the characterization of the consensus sequence is on the basis of homology to known sequences. 
     
     
       5. The method of claim 3 wherein the characterization of the consensus sequence is on the basis of similarities to known sequence motifs. 
     
     
       6. A computer-based iterative method for building putative gene assemblies from a plurality of partial gene sequences, allowing the incremental addition of new partial gene sequences to be integrated with an existing plurality of putative gene assemblies, comprising the steps of: (a) annotating regions within each of the plurality of partial gene sequences and each of the plurality of existing putative gene assemblies;   (b) grouping annotated partial gene sequences with other annotated partial gene sequences, wherein some of the other annotated partial gene sequences may be components of existing putative gene assemblies;   (c) assembling, responsive to grouping relationships, a consensus sequence from the grouped annotated partial gene sequences; and   generating a sequence.   
     
     
       7. The method of claim 6 further comprising the step of: (e) characterizing the consensus sequence.   
     
     
       8. The method of claim 7 wherein the characterization of the consensus sequence is on the basis of homology to known sequences. 
     
     
       9. The method of claim 7 wherein the characterization of the consensus sequence is on the basis of similarities to known sequence motifs. 
     
     
       10. A computer-based iterative method for building putative gene assemblies from a plurality of partial gene sequences, allowing the incremental addition of new partial gene sequences to be integrated with an existing plurality of putative gene assemblies, comprising the steps of: (a) annotating regions within each of the plurality of partial gene sequences and each of the plurality of existing putative gene assemblies;   (b) grouping annotated partial gene sequences with other annotated partial gene sequences, wherein some of the other annotated partial gene sequences may be components of existing putative gene assemblies;   (c) assembling, responsive to grouping relationships, a consensus sequence from the grouped annotated partial gene sequences;   (d) characterizing the consensus sequence; and   (e) generating a sequence.